Webcast Recap: Drugs & Trials for Cancer Diagnostics

         March 5, 2020

Introducing Drugs & Trials for Cancer Diagnostics

VSClinical offers enormous simplicity and consistency in evaluating biomarkers and providing treatment options. Last month, we announced our newest feature to now include the automated collection of relevant clinical trials. The new capability was unveiled in our “Introducing Drugs & Trials for Cancer Diagnostics” webcast with Nathan Fortier, Ph.D., Director of Research, showing the:

  • Identification of relevant clinical evidence for drug sensitivity and resistance based on patient biomarkers and tumor type
  • Review of clinical trial information including inclusion criteria, trial status, and contact information
  • Management of citations associated with relevant, targeted therapies
  • Evaluation of a biomarkers clinical evidence tier based on available evidence for drug sensitivity and resistance

Some Frequently Asked Questions from this webcast:

Can the clinical reports be customized with different logos and content in the headers and footers?

They most definitely can. Each of their reports can be completely customized using a simple Microsoft Word template. You can add your own logos. You can customize the formatting. And you can even select which content you would like to include in the report.

How can multiple people edit the report?

You can share projects across multiple users pretty easily. One way to do this is through a network drive. Alternatively, you can also install VarSeq on a Linux or Windows server and have multiple users have access to that server and you could share data that way.

How often are the trials being updated?

We’re planning on updating all of our clinical trials on a monthly basis. And whenever you select any trial that you’re looking at within VSClinical, it’ll automatically hit the NCT website and pull all of the latest information from clinicaltrials.gov and show it to you. So your report is always going to reflect the latest enrollment status at the time of reporting.

A User’s Perspective: Drugs & Trials for Cancer Diagnostics

Darby Kammeraad, Field Application Scientist Manager, further explained the new capability from a user’s perspective in our March webcast covering topics like:

  • Somatic guidelines inclusion of reporting on clinical trials
  • Discussing the NCI source database clinical trial content
  • Exploring the automated integration of accessing clinical trial content from VSClinical
  • Reviewing example biomarkers to demonstrate the process to report

Some Frequently Asked Questions from this webcast:

Q: Does the clinical trials tab allow you to do a more manual search for a clinical trial rather than the automatic approach?

A: Yes, absolutely it does. There’s a couple of ways to kind of interface with that. If you go to the Search All Trials, you can add that NCT-ID to do a general search for any of the trials that you’d want to. Additionally, what’s nice is once you do a general search for that, we also have that browser that’s integrated too. So you have the capability of not only pulling in all this NCI trial information directly into the VarSeq format, but you can also browse out to that canned content directly from the web browser in the software. Any of these trials that would be in here, you could take that ID field wherever it is on this screen, and then you can basically take that information and enter it as a searchable criteria for the NCT ID directly.

Q: What level of automation can be set up to run through panels for multiple samples, weekly or monthly?

A: There’s definitely a lot of factors that go into that. Basically, we give you a small exposure here with the earlier slide talking about the full-stack architecture. So if users let’s say they’re starting from scratch, you do have the ability to go from FASTQ and even pair that, what would be a Sentieon script for the variant calling in the alignment steps to produce the VCF and BAM to leverage another batch script platform which we have, which is VSPipeline.

And so once you go through and you build a workflow like we were looking at before with the filter chain, you can go to File > Save Project as Template. You utilize that template as a standard protocol for how you want to process your variants. And then VSPipeline and Sentieon, for example, can be paired together so that you can basically drop a FASTQ file into a directory. Everything would automatically process and you can get a finished project read, go through and deep-dive into the variant interpretation and classification much like we were doing with the AMP guidelines getting down to that final clinic report. And in the context I could tell you from experience, it’s almost difficult to measure gene panels in terms of speed because it’s so lightning fast, it’s all within minutes so that a time-to-final project can be, you know, even final report can be well within an hour, even from multiple samples. So that’s a lot of efficiency of once you create a standard pipeline that’s going to be in place, everything’s good to go, the only thing you’re working off of is getting those final biomarkers processed and in that clinical report, it becomes highly efficient. And there’s a lot of details to that every step along that process. But we’d be more than happy to schedule a call with the support team if you wanted to deep dive about how automated you can make your workflow.

Q: Is there a capability in customizing the report format?

A: Yes, absolutely, so I kind of showed you a final report that was rendered. But if we go to the report tab here, we do ship a new report template that comes with the software. And you can see that here, cancer with drugs and trials template V1 one, this will be available with that new release. But you can essentially go in and open up these template files themselves and you can go in and modify these however you’d want to. So, you know, delete any fields, reorganize this or whatever your final form that you would want to have, you have full control of what the layout would be, a lab logo, more involved reorganization of the template itself. And again, if you ever want to get on a call with the FAS, we’d be more than happy to take you to that process and help you achieve your goals and get to that final report template that you would want to standardize. So, yeah, there is a lot of customization capability in here.

We hope you found these webcasts to be useful in learning more about our new drugs & trials capability. If you are interested in seeing VSClinical in a more personalized demo for your organization, please reach out to our team and we will be more than happy to schedule a call with you. Or, if you have any additional questions not covered here, please enter them down below!

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